Conflict of interest
The authors declare that they have no competing interests.
References
Blais, J., Lavoie, S. B., Giroux, S., Bussières, J., Lindsay, C., Dionne, J., . . . Rousseau, F. (2015). Risk of misdiagnosis due to allele dropout and false-positive PCR artifacts in molecular diagnostics: analysis of 30,769 genotypes. J Mol Diagn ,17 (5), 505-514. doi:10.1016/j.jmoldx.2015.04.004
Bohnert, S., Heck, L., Gruber, C., Neumann, H., Distler, U., Tenzer, S., . . . Jacob, S. (2019). Fungicide resistance toward fludioxonil conferred by overexpression of the phosphatase gene MoPTP2 inMagnaporthe oryzae . Mol Microbiol, 111 (3), 662-677. doi:10.1111/mmi.14179
Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data.Bioinformatics, 30 (15), 2114-2120. doi:10.1093/bioinformatics/btu170
Bonizzoni, M., Ochomo, E., Dunn, W. A., Britton, M., Afrane, Y., Zhou, G., . . . Yan, G. (2015). RNA-seq analyses of changes in the Anopheles gambiae transcriptome associated with resistance to pyrethroids in Kenya: identification of candidate-resistance genes and candidate-resistance SNPs. Parasit Vectors, 8 , 474. doi:10.1186/s13071-015-1083-z
Consortium, T. A. g. G. (2017). Genetic diversity of the African malaria vector Anopheles gambiae . Nature, 552 (7683), 96-100. doi:10.1038/nature24995
Costa, V., Angelini, C., De Feis, I., & Ciccodicola, A. (2010). Uncovering the complexity of transcriptomes with RNA-Seq. J Biomed Biotechnol, 2010 , 853916. doi:10.1155/2010/853916
David, J. P., Faucon, F., Chandor-Proust, A., Poupardin, R., Riaz, M. A., Bonin, A., . . . Reynaud, S. (2014). Comparative analysis of response to selection with three insecticides in the dengue mosquito Aedes aegypti using mRNA sequencing. BMC Genomics, 15 , 174. doi:10.1186/1471-2164-15-174
De Wit, P., Pespeni, M. H., & Palumbi, S. R. (2015). SNP genotyping and population genomics from expressed sequences - current advances and future possibilities.Mol Ecol, 24 (10), 2310-2323. doi:10.1111/mec.13165
Després, L., Stalinski, R., Tetreau, G., Paris, M., Bonin, A., Navratil, V., . . . David, J. P. (2014). Gene expression patterns and sequence polymorphisms associated with mosquito resistance to Bacillus thuringiensis israelensis toxins. BMC Genomics , 15 , 926. doi:10.1186/1471-2164-15-926
Faucon, F., Gaude, T., Dusfour, I., Navratil, V., Corbel, V., Juntarajumnong, W., . . . David, J. P. (2017). In the hunt for genomic markers of metabolic resistance to pyrethroids in the mosquitoAedes aegypti : An integrated next-generation sequencing approach.PLoS Negl Trop Dis, 11 (4), e0005526. doi:10.1371/journal.pntd.0005526
Ferguson, S., & Pineda, O. (2010). Putative polymerase chain reaction markers for insecticide resistance in the leafminer Liriomyza trifolii (Diptera: Agromyzidae) to cyromazine and abamectin. J Econ Entomol, 103 (6), 2197-2203. doi:10.1603/ec10073
Ffrench-Constant, R. H. (2013). The molecular genetics of insecticide resistance. Genetics, 194 (4), 807-815. doi:10.1534/genetics.112.141895
Gould, F., Brown, Z. S., & Kuzma, J. (2018). Wicked evolution: Can we address the sociobiological dilemma of pesticide resistance? Science, 360 (6390), 728-732. doi:10.1126/science.aar3780
Guo, D., Luo, J., Zhou, Y., Xiao, H., He, K., Yin, C., . . . Li, F. (2017). ACE: an efficient and sensitive tool to detect insecticide resistance-associated mutations in insect acetylcholinesterase from RNA-Seq data. BMC Bioinformatics , 18 (1), 330. doi:10.1186/s12859-017-1741-6
Guo, L., Liang, P., Zhou, X., & Gao, X. (2014). Novel mutations and mutation combinations of ryanodine receptor in a chlorantraniliprole resistant population of Plutella xylostella (L.). Sci Rep, 4 , 6924. doi:10.1038/srep06924
Hirata, K., Jouraku, A., Kuwazaki, S., Shimomura, H., & Iwasa, T. (2017). Studies on Aphis gossypiicytochrome P450s CYP6CY22 and CYP6CY13 using an in vitro system. J Pestic Sci, 42 (3), 97-104. doi:10.1584/jpestics.D17-006
Hirata, K., Kiyota, R., Matsuura, A., Toda, S., Yamamoto, A., & Iwasa, T. (2015). Association between the R81T mutation in the nicotinic acetylcholine receptor β1 subunit of Aphis gossypiiand the differential resistance to acetamiprid and imidacloprid. J Pestic Sci, 40 (1), 25-31. doi:10.1584/jpestics.D14-092
Hirayama, H., Kageyama, S., Moriyasu, S., Sawai, K., Onoe, S., & Minamihashi, A. (2010). The possibility of a false positive arising from sperm DNA in genetic diagnosis of bovine embryos. J Reprod Dev ,56 (1), 182-186. doi:10.1262/jrd.09-095n
Kim, K. H., Kabir, E., & Jahan, S. A. (2017). Exposure to pesticides and the associated human health effects. Sci Total Environ, 575 , 525-535. doi:10.1016/j.scitotenv.2016.09.009
Kogenaru, S., Qing, Y., Guo, Y., & Wang, N. (2012). RNA-seq and microarray complement each other in transcriptome profiling. BMC Genomics , 13 , 629. doi:10.1186/1471-2164-13-629
Langdon, W. B. (2015). Performance of genetic programming optimised Bowtie2 on genome comparison and analytic testing (GCAT) benchmarks. BioData Min, 8 (1), 1. doi:10.1186/s13040-014-0034-0
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., . . . Genome Project Data Processing, S. (2009). The Sequence Alignment/Map format and SAMtools.Bioinformatics, 25 (16), 2078-2079. doi:10.1093/bioinformatics/btp352
Li, Q., Fang, Y., Li, X., Zhang, H., Liu, M., Yang, H., . . . Wang, Y. (2013). Mechanism of the plant cytochrome P450 for herbicide resistance: a modelling study. J Enzyme Inhib Med Chem, 28 (6), 1182-1191. doi:10.3109/14756366.2012.719505
Li, X., Li, R., Zhu, B., Gao, X., & Liang, P. (2018). Overexpression of cytochrome P450 CYP6BG1 may contribute to chlorantraniliprole resistance in Plutella xylostella (L.). Pest Manag Sci, 74 (6), 1386-1393. doi:10.1002/ps.4816
Love, M. I., Huber, W., & Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol, 15 (12), 550. doi:10.1186/s13059-014-0550-8
Mackenzie-Impoinvil, L., Weedall, G. D., Lol, J. C., Pinto, J., Vizcaino, L., Dzuris, N., . . . Lenhart, A. (2019). Contrasting patterns of gene expression indicate differing pyrethroid resistance mechanisms across the range of the New World malaria vector Anopheles albimanus . PLoS One , 14 (1), e0210586. doi:10.1371/journal.pone.0210586
Mamidala, P., Wijeratne, A. J., Wijeratne, S., Kornacker, K., Sudhamalla, B., Rivera-Vega, L. J., . . . Mittapalli, O. (2012). RNA-Seq and molecular docking reveal multi-level pesticide resistance in the bed bug. BMC Genomics, 13 , 6. doi:10.1186/1471-2164-13-6
Mantione, K. J., Kream, R. M., Kuzelova, H., Ptacek, R., Raboch, J., Samuel, J. M., & Stefano, G. B. (2014). Comparing bioinformatic gene expression profiling methods: microarray and RNA-Seq. Med Sci Monit Basic Res , 20 , 138-142. doi:10.12659/MSMBR.892101
Mavridis, K., Wipf, N., Medves, S., Erquiaga, I., Muller, P., & Vontas, J. (2019). Rapid multiplex gene expression assays for monitoring metabolic resistance in the major malaria vector Anopheles gambiae . Parasit Vectors, 12 (1), 9. doi:10.1186/s13071-018-3253-2
Network, R. P. (2016). Trends and challenges in pesticide resistance detection. Trends Plant Sci, 21 (10), 834-853. doi:10.1016/j.tplants.2016.06.006
Oerke, E. C. (2005). Crop losses to pests. J Agric Sci, 144 (1), 31-43. doi:10.1017/s0021859605005708
Thomas, C. P., Ralf N. (2015). IRAC: Mode of action classification and insecticide resistance management. Pestic Biochem Physiol, 121, 122-128. doi:10.1016/j.pestbp.2014.11.014
Sonoda, S. (2010). Molecular analysis of pyrethroid resistance conferred by target insensitivity and increased metabolic detoxification in Plutella xylostella . Pest Manag Sci, 66 (5), 572-575. doi:10.1002/ps.1918
Tang, W., Wang, D., Wang, J., Wu, Z., Li, L., Huang, M., . . . Yan, D. (2018). Pyrethroid pesticide residues in the global environment: An overview. Chemosphere, 191 , 990-1007. doi:10.1016/j.chemosphere.2017.10.115
Wagih, O. (2017). ggseqlogo: a versatile R package for drawing sequence logos. Bioinformatics, 33 (22), 3645-3647. doi:10.1093/bioinformatics/btx469
Yan, H. H., Xue, C. B., Li, G. Y., Zhao, X. L., Che, X. Z., & Wang, L. L. (2014). Flubendiamide resistance and Bi-PASA detection of ryanodine receptor G4946E mutation in the diamondback moth (Plutella xylostella L.). Pestic Biochem Physiol, 115 , 73-77. doi:10.1016/j.pestbp.2014.09.003
Yan, L., Yang, P., Jiang, F., Cui, N., Ma, E., Qiao, C., & Cui, F. (2012). Transcriptomic and phylogenetic analysis of Culex pipiens quinquefasciatus for three detoxification gene families. BMC Genomics, 13 , 609. doi:10.1186/1471-2164-13-609
Yin, C., Shen, G., Guo, D., Wang, S., Ma, X., Xiao, H., . . . Li, F. (2016). InsectBase: a resource for insect genomes and transcriptomes. Nucleic Acids Res, 44 (D1), D801-807. doi:10.1093/nar/gkv1204
Zhu, B., Xu, M., Shi, H., Gao, X., & Liang, P. (2017). Genome-wide identification of lncRNAs associated with chlorantraniliprole resistance in diamondback moth Plutella xylostella (L.). BMC Genomics, 18 (1), 380. doi:10.1186/s12864-017-3748-9